Trait decoupling promotes evolutionary diversification of the trophic and acoustic system of damselfishes

Genetic regulators of a resource polyphenism interact to couple predatory morphology and behaviour

Phenotypic plasticity often requires the coordinated response of multiple traits observed individually as morphological, physiological or behavioural. The integration, and hence functionality, of this response may be influenced by whether and how these component traits share a genetic basis. In the case of polyphenism, or discrete plasticity, at least part of the environmental response is categorical, offering a simple readout for determining whether and to what degree individual components of a plastic response can be decoupled. Here, we use the nematode Pristionchus pacificus, which has a resource polyphenism allowing it to be a facultative predator of other nematodes, to understand the genetic integration of polyphenism. The behavioural and morphological consequences of perturbations to the polyphenism's genetic regulatory network show that both predatory activity and ability are strongly influenced by morphology, different axes of morphological variation are associated with different aspects of predatory behaviour, and rearing environment can decouple predatory morphology from behaviour. Further, we found that interactions between some polyphenism-modifying genes synergistically affect predatory behaviour. Our results show that the component traits of an integrated polyphenic response can be decoupled and, in principle, selected upon individually, and they suggest that multiple routes to functionally comparable phenotypes are possible.

Small body size is associated with increased evolutionary lability of wing skeleton proportions in birds

Birds are represented by 11,000 species and a great variety of body masses. Modular organisation of trait evolution across birds has facilitated simultaneous adaptation of different body regions to divergent ecological requirements. However, the role modularity has played in avian body size evolution, especially small-bodied, rapidly evolving and diverse avian subclades, such as hummingbirds and songbirds, is unknown. Modularity is influenced by the intersection of biomechanical restrictions, adaptation, and developmental controls, making it difficult to uncover the contributions of single factors such as body mass to skeletal organisation. We develop a novel framework to decompose this complexity, assessing factors underlying the modularity of skeletal proportions in fore-limb propelled birds distributed across a range of body masses. We demonstrate that differences in body size across birds triggers a modular reorganisation of flight apparatus proportions consistent with biomechanical expectations. We suggest weakened integration within the wing facilitates radiation in small birds. Our framework is generalisable to other groups and has the capacity to untangle the multi-layered complexity intrinsic to modular evolution.

Evolutionary modularity, integration and disparity in an accretionary skeleton: analysis of venerid Bivalvia

Modular evolution, the relatively independent evolution of body parts, may promote high morphological disparity in a clade. Conversely, integrated evolution via stronger covariation of parts may limit disparity. However, integration can also promote high disparity by channelling morphological evolution along lines of least resistance-a process that may be particularly important in the accumulation of disparity in the many invertebrate systems having accretionary growth. We use a time-calibrated phylogenetic hypothesis and high-density, three-dimensional semilandmarking to analyse the relationship between modularity, integration and disparity in the most diverse extant bivalve family: the Veneridae. In general, venerids have a simple, two-module parcellation of their body that is divided into features of the calcium carbonate shell and features of the internal soft anatomy. This division falls more along developmental than functional lines when placed in the context of bivalve anatomy and biomechanics. The venerid body is tightly integrated in absolute terms, but disparity appears to increase with modularity strength among subclades and ecologies. Thus, shifts towards more mosaic evolution beget higher morphological variance in this speciose family.

Phylogeny of the damselfishes (Pomacentridae) and patterns of asymmetrical diversification in body size and feeding ecology

The damselfishes (family Pomacentridae) inhabit near-shore communities in tropical and temperature oceans as one of the major lineages in coral reef fish assemblages. Our understanding of their evolutionary ecology, morphology and function has often been advanced by increasingly detailed and accurate molecular phylogenies. Here we present the next stage of multi-locus, molecular phylogenetics for the group based on analysis of 12 nuclear and mitochondrial gene sequences from 345 of the 422 damselfishes. The resulting well-resolved phylogeny helps to address several important questions about higher-level damselfish relationships, their evolutionary history and patterns of divergence. A time-calibrated phylogenetic tree yields a root age for the family of 55.5 mya, refines the age of origin for a number of diverse genera, and shows that ecological changes during the Eocene-Oligocene transition provided opportunities for damselfish diversification. We explored the idea that body size extremes have evolved repeatedly among the Pomacentridae, and demonstrate that large and small body sizes have evolved independently at least 40 times and with asymmetric rates of transition among size classes. We tested the hypothesis that transitions among dietary ecotypes (benthic herbivory, pelagic planktivory and intermediate omnivory) are asymmetric, with higher transition rates from intermediate omnivory to either planktivory or herbivory. Using multistate hidden-state speciation and extinction models, we found that both body size and dietary ecotype are significantly associated with patterns of diversification across the damselfishes, and that the highest rates of net diversification are associated with medium body size and pelagic planktivory. We also conclude that the pattern of evolutionary diversification in feeding ecology, with frequent and asymmetrical transitions between feeding ecotypes, is largely restricted to the subfamily Pomacentrinae in the Indo-West Pacific. Trait diversification patterns for damselfishes across a fully resolved phylogeny challenge many recent general conclusions about the evolution of reef fishes.

What does modularity mean?

Modularity is now generally recognized as a fundamental feature of organisms, one that may have profound consequences for evolution. Modularity has recently become a major focus of research in organismal biology across multiple disciplines including genetics, developmental biology, functional morphology, population and evolutionary biology. While the wealth of new data, and also new theory, has provided exciting and novel insights, the concept of modularity has become increasingly ambiguous. That ambiguity is underlain by diverse intuitions about what modularity means, and the ambiguity is not merely about the meaning of the word-the metrics of modularity are measuring different properties and the methods for delimiting modules delimit them by different, sometimes conflicting criteria. The many definitions, metrics and methods can lead to substantial confusion not just about what modularity means as a word but also about what it means for evolution. Here we review various concepts, using graphical depictions of modules. We then review some of the metrics and methods for analyzing modularity at different levels. To place these in theoretical context, we briefly review theories about the origins and evolutionary consequences of modularity. Finally, we show how mismatches between concepts, metrics and methods can produce theoretical confusion, and how potentially illogical interpretations can be made sensible by a better match between definitions, metrics, and methods.

Integration drives rapid phenotypic evolution in flatfishes

Evolutionary innovations are scattered throughout the tree of life, and have allowed the organisms that possess them to occupy novel adaptive zones. While the impacts of these innovations are well documented, much less is known about how these innovations arise in the first place. Patterns of covariation among traits across macroevolutionary time can offer insights into the generation of innovation. However, to date, there is no consensus on the role that trait covariation plays in this process. The evolution of cranial asymmetry in flatfishes (Pleuronectiformes) from within Carangaria was a rapid evolutionary innovation that preceded the colonization of benthic aquatic habitats by this clade, and resulted in one of the most bizarre body plans observed among extant vertebrates. Here, we use three-dimensional geometric morphometrics and a phylogenetic comparative toolkit to reconstruct the evolution of skull shape in carangarians, and quantify patterns of integration and modularity across the skull. We find that the evolution of asymmetry in flatfishes was a rapid process, resulting in the colonization of novel trait space, that was aided by strong integration that coordinated shape changes across the skull. Our findings suggest that integration plays a major role in the evolution of innovation by synchronizing responses to selective pressures across the organism.

Developmental plasticity reveals hidden fish phenotypes and enables morphospace diversification

The establishment of a given phenotype is only one expression from a range of hidden developmental possibilities. Developmental plasticity at hidden reaction norms might elicit phenotypic diversification under new developmental environments. Current discussion benefits from empirical analyses that integrate multiple environmental stimuli to evaluate how plastic responses may shape phenotypic variation. We raised Megaleporinus macrocephalus fish in different environmental settings to address contributions of developmental plasticity for emergence of new phenotypes and subsequent morphospace diversification. Plastic morphotypes were evaluated at two complementary scales, the M. macrocephalus morphospace and the higher taxonomic level of Anostomidae family. Morphospace analyses demonstrated that developmental plasticity quickly releases distinct head morphotypes that were hidden in the parental monomorphic population. Plastic morphotypes occupied discrete and previously unfilled morphospace regions, a result obtained from comparisons with a control population and in analyses including several Anostomidae species. Plastic responses involved adjustments in shape and relative position of head bonesets, and fish raised under specific environmental combinations rescued phenotypic patterns described for different genera. Therefore, developmental plasticity possibly contributes to adaptive radiation in Anostomidae. Results illustrate how plastic responses enable morphospace diversification and contribute to evolution.

Trait evolution is reversible, repeatable, and decoupled in the soldier caste of turtle ants

The scope of adaptive phenotypic change within a lineage is shaped by how functional traits evolve. Castes are defining functional traits of adaptive phenotypic change in complex insect societies, and caste evolution is expected to be phylogenetically conserved and developmentally constrained at broad phylogenetic scales. Yet how castes evolve at the species level has remained largely unaddressed. Turtle ant soldiers (genus Cephalotes), an iconic example of caste specialization, defend nest entrances by using their elaborately armored heads as living barricades. Across species, soldier morphotype determines entrance specialization and defensive strategy, while head size sets the specific size of defended entrances. Our species-level comparative analyses of morphotype and head size evolution reveal that these key ecomorphological traits are extensively reversible, repeatable, and decoupled within soldiers and between soldier and queen castes. Repeated evolutionary gains and losses of the four morphotypes were reconstructed consistently across multiple analyses. In addition, morphotype did not predict mean head size across the three most common morphotypes, and head size distributions overlapped broadly across all morphotypes. Concordantly, multiple model-fitting approaches suggested that soldier head size evolution is best explained by a process of divergent pulses of change. Finally, while soldier and queen head size were broadly coupled across species, the level of head size disparity between castes was decoupled from both queen head size and soldier morphotype. These findings demonstrate that caste evolution can be highly dynamic at the species level, reshaping our understanding of adaptive morphological change in complex social lineages.

Functional morphogenesis from embryos to adults: Late development shapes trophic niche in coral reef damselfishes

The damselfishes are one of the dominant coral reef fish lineages. Their ecological diversification has involved repeated transitions between pelagic feeding using fast bites and benthic feeding using forceful bites. A highly-integrative approach that combined gene expression assays, shape analyses, and high-speed video analyses was used to examine the development of trophic morphology in embryonic, larval, juvenile, and adult damselfishes. The anatomical characters that distinguish pelagic-feeding and benthic-feeding species do not appear until after larval development. Neither patterns of embryonic jaw morphogenesis, larval skull shapes nor larval bite mechanics significantly distinguished damselfishes from different adult trophic guilds. Analyses of skull shape and feeding performance identified two important transitions in the trophic development of a single species (the orange clownfish; Amphiprion percula): (a) a pronounced transformation in feeding mechanics during metamorphosis; and (b) more protracted cranial remodeling over the course of juvenile development. The results of this study indicate that changes in postlarval morphogenesis have played an important role in damselfish evolution. This is likely to be true for other fish lineages, particularly if they consist of marine species, the majority of which have planktonic larvae with different functional requirements for feeding in comparison to their adult forms.

Buccal venom gland associates with increased of diversification rate in the fang blenny fish Meiacanthus (Blenniidae; Teleostei)

At the macroevolutionary level, many mechanisms have been proposed to explain explosive species diversification. Among them morphological and/or physiological novelty is considered to have a great impact on the tempo and the mode of diversification. Meiacanthus is a genus of Blenniidae possessing a unique buccal venom gland at the base of an elongated canine tooth. This unusual trait has been hypothesized to aid escape from predation and thus potentially play an important role in their pattern of diversification. Here, we produce the first time-calibrated phylogeny of Blenniidae and we test the impact of two morphological novelties on their diversification, i.e. the presence of swim bladder and buccal venom gland, using various comparative methods. We found an increase in the tempo of lineage diversification at the root of the Meiacanthus clade, associated with the evolution of the buccal venom gland, but not the swim bladder. Neither morphological novelty was associated with the pattern of size disparification in blennies. Our results support the hypothesis that the buccal venom gland has contributed to the explosive diversification of Meiacanthus, but further analyses are needed to fully understand the factors sustaining this burst of speciation.

Decoupled diversification dynamics of feeding morphology following a major functional innovation in marine butterflyfishes

The diversity of fishes on coral reefs is influenced by the evolution of feeding innovations. For instance, the evolution of an intramandibular jaw joint has aided shifts to corallivory in Chaetodon butterflyfishes following their Miocene colonization of coral reefs. Today, over half of all Chaetodon species consume coral, easily the largest concentration of corallivores in any reef fish family. In contrast with Chaetodon, other chaetodontids, including the long-jawed bannerfishes, remain less intimately associated with coral and mainly consume other invertebrate prey. Here, we test (i) if intramandibular joint (IMJ) evolution in Chaetodon has accelerated feeding morphological diversification, and (ii) if cranial and post-cranial traits were affected similarly. We measured 19 cranial functional morphological traits, gut length and body elongation for 33 Indo-Pacific species. Comparisons of Brownian motion rate parameters revealed that cranial diversification was about four times slower in Chaetodon butterflyfishes with the IMJ than in other chaetodontids. However, the rate of gut length evolution was significantly faster in Chaetodon, with no group-differences for body elongation. The contrasting patterns of cranial and post-cranial morphological evolution stress the importance of comprehensive datasets in ecomorphology. The IMJ appears to enhance coral feeding ability in Chaetodon and represents a design breakthrough that facilitates this trophic strategy. Meanwhile, variation in gut anatomy probably reflects diversity in how coral tissues are procured and assimilated. Bannerfishes, by contrast, retain a relatively unspecialized gut for processing invertebrate prey, but have evolved some of the most extreme cranial mechanical innovations among bony fishes for procuring elusive prey.

Rates of morphological evolution, asymmetry and morphological integration of shell shape in scallops

Background

Rates of morphological evolution vary across different taxonomic groups, and this has been proposed as one of the main drivers for the great diversity of organisms on Earth. Of the extrinsic factors pertaining to this variation, ecological hypotheses feature prominently in observed differences in phenotypic evolutionary rates across lineages. But complex organisms are inherently modular, comprising distinct body parts that can be differentially affected by external selective pressures. Thus, the evolution of trait covariation and integration in modular systems may also play a prominent role in shaping patterns of phenotypic diversity. Here we investigate the role ecological diversity plays in morphological integration, and the tempo of shell shape evolution and of directional asymmetry in bivalved scallops.

Results

Overall, the shape of both valves and the magnitude of asymmetry of the whole shell (difference in shape between valves) are traits that are evolving fast in ecomorphs under strong selective pressures (gliders, recessers and nestling), compared to low rates observed in other ecomorphs (byssal-attaching, free-living and cementing). Given that different parts of an organism can be under different selective pressures from the environment, we also examined the degree of evolutionary integration between the valves as it relates to ecological shifts. We find that evolutionary morphological integration is consistent and surprisingly high across species, indicating that while the left and right valves of a scallop shell are diversifying in accordance with ecomorphology, they are doing so in a concerted fashion.

Conclusions

Our study on scallops adds another strong piece of evidence that ecological shifts play an important role in the tempo and mode of morphological evolution. Strong selective pressures from the environment, inferred from the repeated evolution of distinct ecomorphs, have influenced the rate of morphological evolution in valve shape and the magnitude of asymmetry between valves. Our observation that morphological integration of the valves making up the shell is consistently strong suggests tight developmental pathways are responsible for the concerted evolution of these structures while environmental pressures are driving whole shell shape. Finally, our study shows that directional asymmetry in shell shape among species is an important aspect of scallop macroevolution.

Electronic supplementary material

The online version of this article (10.1186/s12862-017-1098-5) contains supplementary material, which is available to authorized users.

Contrasting Evolutionary Paths Among Indo-Pacific Pomacentrus Species Promoted by Extensive Pericentric Inversions and Genome Organization of Repetitive Sequences

Pomacentrus (damselfishes) is one of the most characteristic groups of fishes in the Indo-Pacific coral reef. Its 77 described species exhibit a complex taxonomy with cryptic lineages across their extensive distribution. Periods of evolutionary divergences between them are very variable, and the cytogenetic events that followed their evolutionary diversification are largely unknown. In this respect, analyses of chromosomal divergence, within a phylogenetic perspective, are particularly informative regarding karyoevolutionary trends. As such, we conducted conventional cytogenetic and cytogenomic analyses in four Pomacentrus species (Pomacentrus similis, Pomacentrus auriventris, Pomacentrus moluccensis, and Pomacentrus cuneatus), through the mapping of repetitive DNA classes and transposable elements, including 18S rDNA, 5S rDNA, (CA)₁₅, (GA)₁₅, (CAA)₁₀, Rex6, and U2 snDNA as markers. P. auriventris and P. similis, belonging to the Pomacentrus coelestis complex, have indistinguishable karyotypes (2n = 48; NF = 48), with a peculiar syntenic organization of ribosomal genes. On the other hand, P. moluccensis and P. cuneatus, belonging to another clade, exhibit very different karyotypes (2n = 48, NF = 86 and 92, respectively), with a large number of bi-armed chromosomes, where multiple pericentric inversions played a significant role in their karyotype organization. In this sense, different chromosomal pathways followed the phyletic diversification in the Pomacentrus genus, making possible the characterization of two well-contrasting species groups regarding their karyotype features. Despite this, pericentric inversions act as an effective postzygotic barrier in many organisms, which appear to be also the case for P. moluccensis and P. cuneatus; the extensive chromosomal similarities in the two species of P. coelestis complex suggest minor participation of chromosomal postzygotic barriers in the phyletic diversification of these species.

Non-reef environments impact the diversification of extant jacks, remoras and allies (Carangoidei, Percomorpha)

Various factors may impact the processes of diversification of a clade. In the marine realm, it has been shown that coral reef environments have promoted diversification in various fish groups. With the exception of requiem sharks, all the groups showing a higher level of diversity in reefs than in non-reef habitats have diets based predominantly on plankton, algae or benthic invertebrates. Here we explore the pattern of diversification of carangoid fishes, a clade that includes numerous piscivorous species (e.g. trevallies, jacks and dolphinfishes), using time-calibrated phylogenies as well as ecological and morphological data from both extant and fossil species. The study of carangoid morphospace suggests that reef environments played a role in their early radiation during the Eocene. However, contrary to the hypothesis of a reef-association-promoting effect, we show that habitat shifts to non-reef environments have increased the rates of morphological diversification (i.e. size and body shape) in extant carangoids. Piscivory did not have a major impact on the tempo of diversification of this group. Through the ecological radiation of carangoid fishes, we demonstrate that non-reef environments may sustain and promote processes of diversification of different marine fish groups, at least those including a large proportion of piscivorous species.

Functional coupling constrains craniofacial diversification in Lake Tanganyika cichlids

Functional coupling, where a single morphological trait performs multiple functions, is a universal feature of organismal design. Theory suggests that functional coupling may constrain the rate of phenotypic evolution, yet empirical tests of this hypothesis are rare. In fish, the evolutionary transition from guarding the eggs on a sandy/rocky substrate (i.e. substrate guarding) to mouthbrooding introduces a novel function to the craniofacial system and offers an ideal opportunity to test the functional coupling hypothesis. Using a combination of geometric morphometrics and a recently developed phylogenetic comparative method, we found that head morphology evolution was 43% faster in substrate guarding species than in mouthbrooding species. Furthermore, for species in which females were solely responsible for mouthbrooding the males had a higher rate of head morphology evolution than in those with bi-parental mouthbrooding. Our results support the hypothesis that adaptations resulting in functional coupling constrain phenotypic evolution.